Hello Ateequr,

The quickest way to use new genomes with tools is to use them as a custom reference genome. To do this, load the genome in fasta format into your history and set tool form options to use reference genomes "from the history".


Best practices:
1 - double check that the format is strict fasta (all lines wrapped to same length, no extra lines or hidden characters, sequence entries are unique within file).
  2 - use the same genome dataset for all steps within an analysis
  3 - load using FTP and make certain load is complete
      http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP

Hopefully this helps!

Best,

Jen
Galaxy team

On 1/13/12 7:00 AM, Ateequr Rehman wrote:

  Dear Galaxy Administrator

I am analysing transcriptome and genome of clinical
isolatesStenotrophomonasmaltophilia, would be highly obliged if you
could please upload
Stenotrophomonas maltophilia K279 and Stenotrophomonas maltophilia
R551-3 genome
acccesion numbers at NCBI are as following

Stenotrophomonas maltophilia K279 (Accession AM743169)


*Stenotrophomonas maltophilia R551-3*, complete genome
<http://www.ncbi.nlm.nih.gov/nuccore/CP001111.1>

Accession: CP001111


Thanking you all in advance
Ateequr Rehman



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